9K93 | pdb_00009k93

Cryo-EM structure of human signal peptide peptidase like 2A (SPPL2a) in complex with L685,458

PDB DOI: https://doi.org/10.2210/pdb9K93/pdb
EM Map EMD-62186: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Insect expression vector pBlueBachsGCA1
Mutation(s): No

Deposited: 2024-10-25 Released: 2025-10-29
Deposition Author(s): Zhou, R., Huang, G., Guo, X., Wang, J., Ge, X., Shi, Y.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9K93

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into human signal peptide peptidase

Zhou, R., Huang, G., Guo, X., Wang, J., Ge, X., Shi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 58.86 kDa
Atom Count: 2,307
Modeled Residue Count: 282
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptide peptidase-like 2A	A	520	Homo sapiens	Mutation(s): 0 Gene Names: SPPL2A, IMP3, PSL2, PSEC0147 EC: 3.4.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCT8 (Homo sapiens) Explore Q8TCT8 Go to UniProtKB: Q8TCT8
PHAROS: Q8TCT8 GTEx: ENSG00000138600
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TCT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FTO (Subject of Investigation/LOI) Query on FTO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate C₃₉ H₅₂ N₄ O₆ MURCDOXDAHPNRQ-ZJKZPDEISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2020YFA0509300

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.